Team:Edinburgh/Cellulases (C model)

How does this whole synergy thing even work? It can seem almost magical that having enzymes closer together can increase their usefulness, but consider the following statements about cellulose degradation, all of which are true ([http://www.annualreviews.org/doi/abs/10.1146/annurev-biochem-091208-085603 Fontes and Gilbert, 2010])

1. Exoglucanase chews away at the end of a cellulase chain, producing cellobiose sugars.
2. Endoglucanase cuts cellulose chains in the middle, essentially turning one chain into two.
3. Cellobiose inhibits the action of the above enzymes.
4. β-glucosidase cuts cellobiose in half, producing two glucose molecules.

Facts 1 and 2 mean that exoglucanase works best with endoglucanase nearby, since every time endoglucanase acts, it produces new chain-ends for exoglucanase to attack. Meanwhile, facts 1, 3, and 4 mean that β-glucosidase helps nearby copies of the other enzymes by preventing the cellobiose from inhibiting them.

Syn: a simple demonstration of synergy

We can demonstrate that there is (potentially) a huge difference between the synergistic and non-synergistic systems with Edinburgh's Syn C program. This is a 2D simulation that works in the following way:

• The world is a 2D grid.
  • Each spot in the grid can contain a sugar, a bond between sugars, or nothing.
  • The world begins with an array of cellulose.
• Cellulose is modelled as alternating sugars and bonds: s-b-s-b-s-b-s-b-s-b-s etc etc.
• There are three enzyme types: endoglucanase, exoglucanase, and β-glucosidase.
  • The enzymes move about randomly, in a "brownian motion" manner.
  • If an enzyme is in the same place as a bond, it can cut it:
    • Endoglucanase can only cut bonds away from the ends of a chain.
    • Exoglucanase can only cut bonds if this results in a cellobiose molecule (s-b-s) forming.
    • β-glucosidase can only cut cellobiose bonds.
• There is inhibition of exoglucanase by cellobiose; it does not cut bonds (or has a reduced chance to do so) if there is a nearby cellobiose molecule.

Sugars are dark green squares, bonds between sugars are light green. From left to right are shown the actions of endoglucanase, exoglucanase, and β-glucosidase.

Simulating non-synergy vs. synergy

We can run two different simulations with the same settings. However, in one simulation the enzymes float about freely, whereas in the other they travel in triplets, each triplet containing one of each type of enzyme, side by side:

The enzymes' current positions are displayed as white, yellow, or blue squares. Note that in the synergistic system (right) they travel together.

So, what happens if we run a large simulation? This:

Iteration 5000 of a run with 20 copies of each enzyme per simulation. Dark regions are places where the cellulose has been degraded down to free glucose molecules. The left side has 665 free glucose molecules. The right (synergistic) side has 2614.

You can also view an animation of a similar run.

C code

• syn.c
• Makefile

There are two ways to compile Syn. The first is to just compile the C code as it stands. When compiled in this way, there is no graphical display, except that the program saves .bmp graphics files every so often.

However, if you have the SDL graphics library development files (called libsdl1.2-dev in Ubuntu), you can optionally download the Makefile and compile with "make". This version does not (by default) spit out any files; instead, it gives a graphical display of the action as it occurs.

Note that, to work, the Makefile should be called "Makefile" and the C file should be called "syn.c".

There are various constants at the top of the C file that can be experimented with; in particular, the size of the simulation, the number of enzymes present, and the strength of cellobiose inhibition of exoglucanase can all be altered.

Conclusion

Synergy - it actually works!

References

• Fontes CMGA, Gilbert HJ (2010) [http://www.annualreviews.org/doi/abs/10.1146/annurev-biochem-091208-085603 Cellulosomes: highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates]. Annual Review of Biochemistry 79: 655-81 (doi: 10.1146/annurev-biochem-091208-085603).